RQHR Microbiology Test Compendium The Regina Qu’Appelle Health Region (RQHR) Division of Microbiology, within the Department of Laboratory Medicine provides amalgamated service to all patients and providers within RQHR. The laboratory is staffed 24 hours a day, 365 days per year, with medical consultation available 24/7. Contact us: Laboratory Services, Microbiology Regina General Hospital 1440 – 14 Ave Regina, SK S4P 0W5 Phone: 306-766-4481 Fax: 306-766-4640 The Medical Microbiologist on-call can be reached through the hospital switchboards at 306-766-4444 or 306-766-2222. General Specimen Collection and Submission Requirements All specimens must be labeled and submitted with a completed requisition (see Laboratory Services Manual - General Information for further details). Specimens may be rejected if: ● they are improperly labeled or not accompanied by a completed requisition ● submitted in inappropriate container, received in leaking or otherwise compromised container ● Insufficient quantity of specimen, inappropriate specimen type for test requested, duplicate specimens, or if integrity of specimen has been compromised (e.g. lack of temperature control, delays in transit) Whenever possible, specimens for microbiologic detection should be collected before antibiotics are given. Care must be taken to avoid contamination of specimens with organisms of the normal flora or environment. Specimens should be delivered to the laboratory soon after they are collected. Delays in transport can lead to incorrect, invalid, or misleading results. The date and time of specimen collection should be recorded on the requisition in order to identify these delays and aid in results interpretation. Providing relevant clinical information will ensure specimens are processed and reported appropriately. Last revised September 2019
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RQHR Microbiology Test Compendium
The Regina Qu’Appelle Health Region (RQHR) Division of Microbiology, within the Department of
Laboratory Medicine provides amalgamated service to all patients and providers within RQHR.
The laboratory is staffed 24 hours a day, 365 days per year, with medical consultation available 24/7.
Contact us:
Laboratory Services, Microbiology
Regina General Hospital
1440 – 14 Ave
Regina, SK
S4P 0W5
Phone: 306-766-4481
Fax: 306-766-4640
The Medical Microbiologist on-call can be reached through the hospital switchboards at 306-766-4444
or 306-766-2222.
General Specimen Collection and Submission Requirements All specimens must be labeled and submitted with a completed requisition (see Laboratory Services
Manual - General Information for further details). Specimens may be rejected if:
● they are improperly labeled or not accompanied by a completed requisition
● submitted in inappropriate container, received in leaking or otherwise compromised container
● Insufficient quantity of specimen, inappropriate specimen type for test requested, duplicate
specimens, or if integrity of specimen has been compromised (e.g. lack of temperature control,
delays in transit)
Whenever possible, specimens for microbiologic detection should be collected before antibiotics are
given. Care must be taken to avoid contamination of specimens with organisms of the normal flora or
environment.
Specimens should be delivered to the laboratory soon after they are collected. Delays in transport can
lead to incorrect, invalid, or misleading results. The date and time of specimen collection should be
recorded on the requisition in order to identify these delays and aid in results interpretation.
Providing relevant clinical information will ensure specimens are processed and reported appropriately.
For all adult collections, 2 sets collected from 2 separate sites will always be performed. One set should always be collected from a peripheral venipuncture. Label sites of collection.
Bottles are incubated on an automated instrument with continuous monitoring until growth is detected, or for 5 days if negative.
Once growth is detected, Gram stain is performed STAT and bottles are sub-cultured.
Positive gram stains are considered CRITICAL RESULTS and are phoned to submitting location immediately upon detection 24 hours per day.
Identification and susceptibility results are usually available 24 – 48 hours after organism is isolated.
Reports of no growth are sent at 24 hours and 5 days, if applicable.
Adult blood culture bottles must be filled to the appropriate volume in order to achieve optimal dilution of ingredients. Over-filling or under-filling bottles will reduce the sensitivity of detection.
Label bottles and provide information on requisition to identify the source of each blood culture set (e.g. sets labeled #1, #2; requisition indicates #1 venipuncture, #2 PICC line).
Pediatric blood cultures will be drawn as a single set unless specifically ordered as 2 sets. Pediatric blood cultures will not include anaerobic culture bottles unless specifically requested.
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Transport at room temperature, as soon as possible and <24 hours. Do not freeze or refrigerate.
Collect using sterile technique into sterile screw capped containers. Minimum volumes: Bacterial/yeast culture ≥1 mL Fungal culture ≥2 mL Transport at room temperature, as soon as possible and <2 hours. Do not freeze or refrigerate.
Gram stain and culture for bacteria and yeast is performed routinely. Cultures are incubated for 7 days. Filamentous fungal cultures performed if ordered on requisition. Specimen will be forwarded to RRPL for testing. All CSF specimens requesting filamentous fungal culture will have a qualitative Cryptococcal Antigen lateral flow assay (CrAg LFA) performed at RGH. Positive specimens will undergo semi-quantitative titration.
Positive gram stains are considered CRITICAL RESULTS and are phoned to submitting location immediately upon detection 24 hours per day. Identification and susceptibility results are usually available 24 – 48 hours after organism is isolated. Reports of no growth are sent at 24 and 72 hours, if applicable.
Avoid sending first tube collected for microbiology testing due to increased risk of specimen contamination. If ordering additional testing from reference laboratory, ensure adequate volume is submitted: ≥2 mL for Mycobacterial culture, ≥1mL for viral isolation, and approximately 1mL per additional special request
Collect using sterile technique into sterile screw capped container. Alternatively, collect 2 mL into a sterile screw capped container for Gram stain preparation, then inoculate aerobic and anaerobic blood culture bottles with 6 – 8 mL each. Transport at room temperature, as soon as possible and <24 hours. Do not freeze or refrigerate.
Gram stain and culture for aerobic and anaerobic bacteria, and yeast is performed routinely. Cultures are incubated for 7 days. Filamentous fungal cultures performed if ordered on requisition. Specimen will be forwarded to RRPL for testing. Specimens submitted in blood culture bottles are incubated on an automated instrument with continuous monitoring
Positive gram stains are considered CRITICAL RESULTS and are phoned to submitting location immediately upon detection 24 hours per day. Reports of no growth are sent at 24 and 72 hours, if applicable. Specimens submitted in blood culture bottles will have negative reports sent at 24 hours and 5 days.
Swabs of sterile fluid are inappropriate specimens. This significantly compromises the sensitivity of organism detection.
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until growth is detected, or for 5 days if negative.
Intravascular Catheter tip Disinfect surrounding skin before removal. Aseptically remove catheter and cut 1-2” of distal end into sterile container. If an intravascular line infection is suspected, blood cultures should be collected simultaneously. Collect 1 set from suspected intravascular line before removal, and collect 1 set from a peripheral venipuncture. Label sites of collection. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Intravascular catheter tips are processed by a semi-quantitative roll method, and incubated aerobically. Neonate or TPN, culture for Malassezia spp. Will be forwarded to RRPL for testing. CSF shunt and peritoneal dialysis catheter tips are flushed and vortexed with broth, which is then cultured semi-quantitatively. Cultures are incubated aerobically for 4 days.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 96 hours, if applicable.
Submit intravascular catheter tips only if there are signs of infection. Tips from Foley catheters, chest tubes, and other drains are not accepted.
before swabbing affected areas. Avoid touching surrounding skin. Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic bacteria and yeast is performed routinely. Cultures are incubated for 48 hours.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 48 hours, if applicable.
If aspiration of wound is possible, this is preferred as it will more accurately identify pathogens and minimize isolation of colonizing organisms. Note: swabs from decubitus ulcers and pressure sores cannot distinguish infecting pathogens from colonizing organisms and are not routinely processed. Please
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submit tissue or aspirate specimens. Note: swabs are not appropriate for isolation of filamentous fungi
Deep wound swab Clean wound thoroughly before swabbing affected areas. Avoid touching surrounding skin. Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic and anaerobic bacteria, and yeast is performed routinely. Cultures are incubated for 72 hours.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 72 hours, if applicable.
If aspiration of wound or tissue biopsy is possible, this will be preferred as it will more accurately identify pathogens and minimize isolation of colonizing organisms. Note: swabs from decubitus ulcers and pressure sores cannot distinguish infecting pathogens from colonizing organisms and are not routinely processed. Please submit tissue or aspirate specimens. Note: swabs are not appropriate for isolation of filamentous fungi
Aspirate/fluid/drainage Clean and decontaminate surface before collecting specimen. Aspirate ≥1 mL of specimen using sterile technique. Specimen can be submitted to lab in a sterile screw capped container, or in capped syringe with needle removed.
Gram stain and culture for aerobic and anaerobic bacteria, and yeast is performed routinely. Cultures are incubated for 72 hours. Filamentous fungal cultures performed if ordered on requisition. Specimen will be forwarded to RRPL for testing.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 72 hours, if applicable.
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Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
If Actinomycosis is suspected, please indicate under ‘Other/Special Requests’. Cultures will be incubated for 10 days.
Tissue/biopsy Collect using sterile technique, into sterile screw capped container. You may add a small amount of sterile saline to keep tissue from drying out. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic and anaerobic bacteria, and yeast is performed routinely. Cultures are incubated for 7 days. Filamentous fungal cultures performed if ordered on requisition. Specimen will be forwarded to RRPL for testing. If Actinomycosis is suspected, please indicate under ‘Other/Special Requests’. Cultures will be incubated for 10 days.
Positive gram stains are considered CRITICAL RESULTS and are phoned to submitting location immediately upon detection 24 hours per day. Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 hours and 7 days, if applicable.
Bone Chip Collect using sterile technique, and place into sterile screw capped container. Bone bank products may be directly placed into tube of Thioglycollate broth. Transport at room temperature, as soon as possible. Do not freeze or refrigerate.
Gram stain and culture for aerobic and anaerobic bacteria, and yeast is performed routinely. Cultures are incubated for 7 days. Bone bank products are incubated in submitted Thioglycollate broth for 7 days.
Positive gram stains or detection of growth from bone bank specimens are considered CRITICAL RESULTS and are phoned to submitting location immediately upon detection 24 hours per day. Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 hours and 7 days, if applicable.
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Foreign body/implant Collect using sterile technique, and place into sterile screw capped container. Transport at room temperature, as soon as possible. Do not freeze or refrigerate.
Gram stain and culture for aerobic and anaerobic bacteria, and yeast is performed routinely. Cultures are incubated for 7 days.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 hours and 7 days, if applicable.
For unusual specimens or special requests, contact the Microbiologist on-call before submitting to laboratory.
ARO SCREENS MRSA (Methicillin-Resistant Staphylococcus aureus)
Nares: insert into nostril 2-3 cm and roll swab 5 times. Insert same swab into second nostril and repeat. Groin: roll swab from top to bottom of inguinal area 5 times. Repeat using same swab on opposite side. Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Real Time Polymerase Chain Reaction (RT-PCR) testing performed routinely. Newly identified colonization is confirmed with culture.
Turnaround time ≤24 hours. Newly identified colonization confirmation available at 72 hours. Inpatient wards and Infection Control notified immediately of new positive results. New positive cases are reported to Public Health.
Submit screens from nares, groins, invasive devices in place ≥1 month (e.g. tracheostomy, catheters), and open wounds. Only 1 requisition per patient is needed for all MRSA screening specimens. Repeat specimens received <7 days after a negative screen or <30 days after a positive screen will not be processed.
VRE (Vancomycin-Resistant Enterococcus)
Rectal swab: insert into rectum 2-3 cm and rotate 5 times Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs.
Chromogenic screening cultures are performed routinely
Turnaround time 48 – 72 hours. Inpatient wards and Infection Control notified immediately of new positive results. New positive cases are reported to Public Health.
Repeat specimens received <7 days after a negative screen or <30 days after a positive screen will not be processed.
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Stool: collect 1g (~size of a hazelnut) of freshly passed stool into sterile container with no preservative (White top). Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Rectal swab: insert into rectum 2-3 cm and rotate 5 times Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Stool: collect 1g (~size of a hazelnut) of freshly passed stool into sterile container with no preservative (White top). Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Chromogenic screening cultures are performed routinely
Turnaround time 48 – 72 hours. Inpatient wards and Infection Control notified immediately of new positive results. New positive cases are reported to Public Health.
Repeat specimens received <7 days after a negative screen or <30 days after a positive screen will not be processed.
URINE C&S only if positive urinalysis or C&S
Midstream: hold labia apart (female) or retract foreskin (male), begin voiding and discard first several mL urine. Without stopping flow of urine, collect 5 – 10mL
Urinalysis screening performed. If urinalysis is positive for leukocyte esterase (LE) or nitrites, specimen will undergo quantitative culture
Urinalysis results will be reported within 24 hours. If specimen is cultured, organism identification is usually available 24 – 48 hours after it is isolated.
If submitting urine for diagnosis of urinary tract infection (UTI), please order “C&S only if positive urinalysis”. A negative urinalysis has high specificity to rule out UTI. If urinalysis is
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midstream specimen into wide-mouth sterile container. Straight Catheter: thoroughly clean urethral area with mild soap and water. Aseptically insert catheter into bladder. Discard initial several mL urine, collect 5 – 10 mL. Indwelling Catheter: disinfect catheter collection port with 70% alcohol. Use needle and syringe to aseptically collect 5 – 10 mL of urine. Supra-pubic aspirate or Cystoscopy collection: collect 5 – 10 mL using aseptic technique. Transfer urine into tube containing Boric acid preservative and fill to indicator line. Sterile containers may be submitted if processed <2 hours after collection. If ordering “C&S only if positive urinalysis”, submit urine in both sterile container and preservative. Transport at room temperature, as soon as possible. If delay is
for uropathogenic bacteria. Cultures are incubated 24-48 hours. If urinalysis is negative, this predicts the absence of a urinary tract infection. Specimen will not be cultured. If C&S is ordered, urine will be cultured without a urinalysis performed.
Reports of no growth are sent at 24 hours, if applicable.
positive for nitrites or leukocyte esterase culture will be performed routinely. Urine from pregnant women or individuals undergoing GU surgery/manipulation should order a regular urine C&S to ensure appropriate processing. Urine collected or received in non-sterile containers is unacceptable for culture. Catheter bags are not suitable for culture. Specimens collected in pediatric urine bags should be aseptically transferred into sterile container and tube containing Boric acid preservative. Repeat specimens received within 3 days will not be processed.
into clean, dry container. Transfer to enteric transport media container (Cary Blair). Fill to line marked on container. There should be no contaminating material. E.g. urine, tissue paper. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Real Time Polymerase Chain Reaction (RT-PCR) testing performed routinely for the detection of Salmonella sp., Shigella sp., Camplybacter sp., and E. coli shiga- toxin producing (STEC).
Turnaround time ≤24 hours All positive PCR results are sent for confirmation at RRPL. Positive Reports are sent to Public Health.
Repeat specimens received within 5 days will not be processed. Stool cultures are not performed on patients who have been in hospital >3 days. Consider C.difficile testing in hospitalized patients with new onset diarrhea. Susceptibility testing is not routinely performed on enteric pathogens from patients without known risk factors. If antibiotic therapy is indicated, please contact the Microbiology lab at 766-4481.
Clostridium difficile Collect 1g (~size of a hazelnut) of freshly passed stool into sterile container with no preservative. There should be no contaminating material. E.g. urine, tissue paper. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
All stools are initially tested for GDH and Toxin A/B using an enzyme immunoassay (EIA). Specimens with concordant results (i.e. GDH+/Toxin+ or GDH-/Toxin-) are reported immediately. Specimens with discordant results (i.e. GDH+/Toxin-) undergo PCR testing, and results of the PCR assay are reported.
Turnaround time 24 hours. The rate of asymptomatic carriage of C.difficile in young children is high (up to 50% <3 years; up to 74% <1 year). Specimens from children <1 year will not be processed. Positive results in children <3 years should be interpreted with caution. Repeat specimens from patients with previously positive C.difficile <2 weeks will not be tested. Formed stools are not routinely processed. If patient
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is suspected of C.difficile-related ileus, please clearly indicate on requisition or contact the Microbiology lab at 766-4481.
GENITAL TRACT Gonorrhea Cervical: use a speculum
without lubricant to visualize the cervix. Wipe off any mucus or secretions with first swab and discard. Using second swab, insert into the os and rotate. Do not touch the sides of the vaginal canal with the swab. Urethral: insert small urethro-genital swab 2 – 4 cm into urethral lumen, rotate swab, and leave in place for at least 2 seconds. Other acceptable specimens include: rectal, pharyngeal, conjunctival Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. Do not freeze or refrigerate.
Culture for Neisseria gonorrhoeae performed routinely. Gram stains are prepared for conjunctival and male urethral specimens. Cultures are incubated for 72 hours.
Turnaround time 24 – 72 hours. Positive cultures from conjunctival specimens or from patients <13 years of age are considered CRITICAL RESULTS and are phoned to submitting location immediately upon detection 24 hours per day. Positive reports are sent to Public Health.
Culture to diagnose infection with N.gonorrhoeae from the genital tract should generally be accompanied by specimens sent for molecular detection of N.gonorrhoeae and C.trachomatis. Molecular detection has superior sensitivity to culture and is performed at RRPL
Group B Streptococcus (GBS) screen
Collect a swab specimen of the vaginal introitus and anorectum.
Specimen is screened for presence of Streptococcus agalactiae (Group B Streptococcus; GBS).
Turnaround time 24 – 48 hours.
Susceptibility testing is not routinely performed as organism is universally susceptible to first line
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Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
treatment/prophylaxis with beta-lactam antibiotics. If susceptibility testing is required, please clearly indicate on requisition or contact Microbiology Laboratory at 766-4481.
Bacterial Vaginosis & Candida Using a speculum without lubricant, swab vaginal mucosa high in the vaginal canal. Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Direct examination using microscopy is performed routinely
Nugent score (or N score) is reported with interpretation for bacterial vaginosis diagnosis. Presence and quantity of yeast is reported. Turnaround time 24 hours.
Nugent score (or N score) is not validated for the diagnosis of bacterial vaginosis in pre-pubescent or post-menopausal women.
Vaginal culture Using a speculum without lubricant, swab vaginal mucosa high in the vaginal canal or at visibly affected site. Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for Streptococcus pyogenes (Group A Streptococcus, GAS), Staphylococcus aureus, and yeast are performed routinely. Specimens from children <13 years will also be screened for common enteric and respiratory pathogens. Cultures are incubated for 48 hours.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 48 hours, if applicable.
Vaginal cultures are not indicated in the investigation of vaginitis in estrogenized women. Please send specimens for Bacterial Vaginosis & Yeast, Trichomonas and/or Gonorrhea/Chlamydia (performed at RRPL). Children <13 years can occasionally experience vaginal infections due to Salmonella spp., Shigella spp.,
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S.pneumoniae, H.influenzae, and N.meningitidis
Upper Genital Tract Collect specimens using sterile technique, avoiding lower genital tract contamination. Place biopsies into sterile screw capped container. You may add a small amount of sterile saline to keep from drying out. Aspirates can be submitted in a sterile screw capped container, or in capped syringe with needle removed. If using a swab, liquid-based E-swab collection system (preferred) or M-40 Transystem swabs are acceptable. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic and anaerobic bacteria, N.gonorrhoeae, and yeast are performed routinely. Swabs and aspirates are incubated 72 hours; biopsy specimens are incubated up to 7 days. If Actinomycosis is suspected, please indicate under ‘Other/Special Requests’. Cultures will be incubated for 10 days.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 hours and at end of incubation, if applicable.
Aspirate or biopsy specimens will yield more accurate results compared with swabs.
External Genitalia Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic bacteria and yeast are performed routinely. Cultures are incubated for 48 hours.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 48 hours, if applicable.
Note: swabs are not appropriate for isolation of filamentous fungi
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RESPIRATORY TRACT Nasopharyngeal Influenza A/B Using flocked swab, insert
into nostril straight back (not upwards) and into the nasopharynx. The distance from the patient’s nose to their ear gives an estimate of the distance the swab should be inserted. Leave in place for a few seconds, then gently rotate swab to collect epithelial cells and withdraw. Repeating procedure for the second nostril will improve pathogen detection. Place swab in Universal Transport Media (UTM). Break the shaft off at the breakpoint and close vial tightly. Transport at room temperature, as soon as possible.
Nucleic acid amplification test (NAAT, or PCR) detecting Influenza A, Influenza B.
Results reported as Positive or Negative Routine testing will be performed within 24 hours of receipt in laboratory. STAT testing is available within 4 hours. Positive results are sent to Public Health.
This testing is routinely available only for inpatients during influenza season (as determined by Public Health). Requests from outpatients or outside of influenza season will be forwarded to the Roy Rowmanow Provincial Laboratory (RRPL) for full NAAT respiratory panel testing. All specimens tested at RGH Microbiology will subsequently be forwarded to RRPL for full NAAT respiratory panel testing.
Pediatric Auger Suction Using a syringe and tubing, push a small amount of sterile saline into the nose, then apply gentle suction to collect aspirate. Submit specimen in sterile, screw-capped container. Small volumes may be left in tubing, with tubing submitted in sterile container.
Gram stain and culture for aerobic bacteria and yeast are performed routinely. Cultures are incubated for 48 hours.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 48 hours, if applicable.
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Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Sinus Aspirate bacterial C&S Collect invasive specimen at time of nasal endoscopy or by needle puncture and aspiration of sinuses. Submit specimen in sterile, screw-capped container. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic and anaerobic bacteria and yeast are performed routinely. Cultures are incubated for 72 hours. Filamentous fungal cultures performed if ordered on requisition. Specimen will be forwarded to RRPL for testing.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 72 hours, if applicable.
Nasal swabs, nasal secretions, or swabs of secretions will not be cultured.
Nasal Staphylococcus aureus carriage screen
Insert into nostril 2-3 cm and roll swab 5 times. Insert same swab into second nostril and repeat. Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Culture for Staphylococcus aureus is performed routinely. If positive, isolates are screened for methicillin-resistance (MRSA). Cultures are incubated for 24 hours.
Turnaround time 24 hours. Screening for MRSA reported at 48 hours.
Mouth swabs (buccal mucosa, tongue, or oropharynx)
Scrape area with tongue depressor to remove plaque, then swab to collect specimen
Gram smear is performed. Turnaround time 24 hours.
If Candida susceptibility testing is required please clearly indicate on requisition or contact Microbiology Laboratory at 766-4481.
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Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Throat swab – GASS Depress tongue gently with a tongue depressor. Sample the posterior pharynx, tonsils, and inflamed areas with swab. Avoid touching the oral mucosa or tongue with the swab. Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Specimen is cultured on Chromogenic media for Streptococcus pyogenes (Group A Streptococcus, GASS) is performed routinely.
Turnaround time 24-48 hours. Reports of no/non-significant growth are sent at 24 and 48 hours, if applicable.
Repeat specimens received within a 24 hour period are not processed. Susceptibility testing is not routinely performed as organism is universally susceptible to first line treatment with beta-lactam antibiotics. If susceptibility testing is required, please clearly indicate on requisition or contact Microbiology Laboratory at 766-4481.
Throat swab – other Depress tongue gently with a tongue depressor. Sample the posterior pharynx, tonsils, and inflamed areas with swab. Avoid touching the oral mucosa or tongue with the swab. Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs.
Culture for aerobic bacteria is performed routinely. Cultures are incubated for 48 hours.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no/non-significant growth are sent at 24 and 48 hours, if applicable.
If patient has cystic fibrosis, indicate clearly on requisition Final report is issued after 5 days.
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Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Sputum Have patient rinse mouth or gargle with water before specimen collection to remove contaminating material and organisms. Patient must cough deeply so that exudative material is obtained from the lung; saliva and nasal drainage are inadequate specimens. Deep coughing may be induced by inhalation of an aerosol of warm, hypertonic (5-15%) saline (label as “Induced” if collected this way). Submit sample volume of 5 – 10mL in sterile, screw-capped container. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic bacteria and yeast is performed routinely. Cultures are incubated for 48 hours. Filamentous fungal cultures performed if ordered on requisition. Specimen is sent to RRPL for testing.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no/non-significant growth are sent at 24 and 48 hours, if applicable.
Sputum specimens are screened to assess the amount of oropharyngeal contamination before culturing. Specimens grossly contaminated by the upper respiratory tract, including salivary specimens, are not cultured. Repeat specimens for routine culture received within a 3 day period are not routinely processed, unless originating from an intensive care unit.
Endotracheal tube (ETT) suction
Collect sputum samples from patients with tracheostomies and endotracheal tubes using a suction device and a sterile sputum trap.
Gram stain and culture for aerobic bacteria and yeast is performed routinely. Cultures are incubated for 48 hours. Filamentous fungal cultures performed if ordered on
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated.
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Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
requisition. Specimen is sent to RRPL for testing
Reports of no growth are sent at 24 and 48 hours, if applicable.
Bronchial wash During bronchoscopy, wash bronchus with sterile, normal saline (or other physiologic solution). Collect washing fluid into sterile screw-capped container. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and quantitative culture for aerobic bacteria and yeast is performed routinely. Cultures are incubated for 48 hours. Filamentous fungal cultures performed if ordered on requisition. Specimen is sent to RRPL for testing.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 48 hours, if applicable.
Bronchial washings submitted from the same patient, from the same procedure are pooled for routine microbiologic processing.
Brochoalveolar lavage During bronchoscopy, lavage distal airways and alveoli with sterile, normal saline (or other physiologic solution). Collect lavage fluid into sterile screw-capped container. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and quantitative culture for aerobic bacteria and yeast is performed routinely. Cultures are incubated for 48 hours. Filamentous fungal cultures performed if ordered on requisition. Specimen is sent to RRPL for testing.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 48 hours, if applicable.
Protected Brush Specimen During bronchoscopy, use protected brush to directly sample respiratory tract. Place protected brush-catheter into sterile screw-capped container. Transport at room temperature, as soon as
Gram stain and quantitative culture for aerobic bacteria and yeast is performed routinely. Cultures are incubated for 48 hours. Filamentous fungal cultures performed if ordered on
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 and 48 hours, if applicable.
Protected Brush Specimens have the greatest yield isolating pathogens, compared to other invasively-collected respiratory specimens (i.e. bronchial wash, bronchoalveolar lavage)
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possible. If delay is anticipated, keep specimen at 4°C.
requisition. Specimen is sent to RRPL for testing.
Lung Biopsy Collect using sterile technique (transthoracic) or minimize contamination from upper respiratory tract (transbronchial), into sterile screw capped container. You may add a small amount of sterile saline to keep tissue from drying out. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic and anaerobic bacteria, and yeast is performed routinely. Cultures are incubated for 7 days. Filamentous fungal cultures performed if ordered on requisition. Specimen is sent to RRPL for testing. If Actinomycosis is suspected, please indicate under ‘Other/Special Requests’. Cultures will be incubated for 10 days.
Positive gram stains are considered CRITICAL RESULTS and are phoned to submitting location immediately upon detection 24 hours per day. Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 hours and 7 days, if applicable.
EARS/EYES Eyes – conjunctiva Cleanse skin around eye.
Make-up or ointment should be removed with sterile cotton and saline. Swab the conjunctiva around the inner canthus or cul-de-sac. Lower the bottom eyelid and apply the swab tip to the lower bulbar conjunctiva for about 5 seconds, without touching the eyelid margin. Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs.
Gram stain and culture for aerobic bacteria and yeast is performed routinely. Cultures are incubated for 48 hours. Culture for Neisseria gonorrhoeae will be performed if ordered on requisition. Specimens from infants <2 months will automatically be cultured for N.gonorrhoeae. Cultures are incubated for 72 hours.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 hours and 48 hours, if applicable.
Swabs from both the infected and uninfected eye need to be submitted. Clearly indicate which eye is affected.
Last revised September 2019
Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Eyes – invasive Collect vitreous/aqueous fluid and corneal specimens using sterile technique. Specimen can be submitted to lab in a sterile container, or in capped syringe with needle removed. Eye Packs are available for ophthalmology to directly inoculate media at site of collection. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic and anaerobic bacteria. Fluorescent stain and culture for yeast and filamentous fungi is performed routinely at RRPL and inoculate media will be forwarded after Bacterial culture is performed at RGH. Bacterial cultures are incubated for 7 days.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 hours and 72 hours, if applicable.
If infection with amoeba suspected, please consult with the Medical Microbiologist on-call.
Ears – external canal Cleanse external canal with mild detergent prior to swabbing affected area, touching only the discharge from deeper areas or active margin. Use liquid-based E-swab collection system (preferred) or M-40 Transystem swabs. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic bacteria and yeast is performed routinely. Cultures are incubated for 48 hours.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 hours and 48 hours, if applicable.
Samples from the external ear are appropriate for the diagnosis of otitis externa only, and not recommended in the evaluation of otitis media.
Last revised September 2019
Ears – invasive Collect surgical or tympanocentesis specimens into sterile container. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Gram stain and culture for aerobic and anaerobic bacteria and yeast is performed routinely. Cultures are incubated for 72 hours.
Identification and susceptibility results are usually available 24 – 48 hours after an organism is isolated. Reports of no growth are sent at 24 hours and 72 hours, if applicable.
Acceptable specimens include spontaneous or induced sputum, bronchoalveolar lavage, and bronchial wash. Collect specimens as described above; minimum volume required 4 mL. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
Nucleic acid amplification test (NAAT, or PCR) performed using Cepheid GeneXpert MTB/RIF®
Results will be reported as Positive or Negative for detection of M.tuberculosis. Routine testing will be performed within 24 hours of receipt in laboratory. STAT testing is available within 4 hours. Positive results are sent to Public Health and Saskatchewan TB Control.
Testing is routinely available for inpatient settings only. PCR testing is indicated on one specimen per diagnostic evaluation, estimated by once per 6 months. Additional specimens will be forwarded to RRPL for acid fast bacilli (AFB) microscopy and mycobacterial culture. All specimens undergoing TB PCR testing will subsequently be forwarded to RRPL for AFB microscopy and mycobacterial culture. This assay can be used to support discontinuation of airborne isolation precautions in hospitalized patients, as its sensitivity is comparable to 3 sputum smears. However, this assay does not replace culture-based diagnostics. Mycobacterial culture of 3
Last revised September 2019
specimens is required to rule out the diagnosis of active TB.
Cryptococcal Antigen CSF: collect using sterile technique, into sterile screw capped container. Minimum volume ≥2 mL Transport at room temperature, as soon as possible and <2 hours. Do not freeze or refrigerate. Testing can also be performed on serum collected in SST. Transport at room temperature.
Cryptococcal Antigen lateral flow assay (CrAg LFA) is performed. Positive specimens will undergo semi-quantitative titration.
Results will be reported as Positive or Negative for detection of Cryptococcal antigen. Positive specimens will have titer reported.
CSF specimens requesting Cryptococcal Antigen testing will also be forwarded to RRPL for fungal cultures. CSF specimens requesting fungal culture will also have Cryptococcal Antigen testing performed first, then sent to RRPL for fungal cultures.
Pneumocystis jirovecii (previously Pneumocystic carinii pneumonia or PCP)
Acceptable specimens include spontaneous or induced sputum, bronchoalveolar lavage, and bronchial wash. Collect specimens as described above; minimum volume required 1 mL. Transport at room temperature, as soon as possible. If delay is anticipated, keep specimen at 4°C.
PCR testing is performed. All positive results are to be repeated and then examined under a fluorescent Microscopy.
Turnaround time 24 – 72 hours
Repeat testing of sputa for Pneumocystis jirovecii does not significantly increase diagnostic yield and delays definitive diagnosis. In HIV positive patients, a bronchoalveolar lavage is indicated after the first negative sputum. In HIV negative patients, sputa have very low sensitivity and bronchoalveolar lavage should be considered as a primary diagnostic specimen.
Person Under Investigation of Level 4 Infection, including Ebola Virus Disease or novel emerging pathogens
DO NOT COLLECT ROUTINE SPECIMENS
CONTACT MICROBIOLOGIST ON-CALL THROUGH HOSPITAL SWITCHBOARD
Last revised September 2019
TESTING PROVIDED THROUGH THE Roy Romanow Provincial Laboratory (RRPL)
Refer to RRPL on-line compendium http://sdcl-testviewer.ehealthsask.ca/
Mycobacterium culture/AFB culture Bedbugs identification BK virus Mycoplasma/Ureaplasma genital culture
Blastomyces serology/Fungal Serology Borrelia burgdorferi serology (IgG/IgM) Borrelia burgdorferi PCR Chlamydophyla pneumonia serology (IgG/IgM) EBV viral load Echinococcosis serology/Parasitology serology Respiratory Screen by NAAT Parvovirus serology (IgG/IgM) Filariasis serology/parasitology serology Fleas- ectoparasite identification Rash panel- serology Voriconazole level Food borne illness outbreak-food samples Gonorrhea and Chlamydia/ Trichomonas STD panel NAAT Hantavirus- serology Hepatitis A IgM/IgG Hepatitis B surface Ab, surface Ag, core Ab, e Ab, e Ag
Hepatitis B viral load Hepatitis C Antibody Hepatitis C viral load Hepatitis C genotyping HSV type 1 and 2 serology (IgG) HSV PCR H pylori serology (IgG) H. pylori cultures HIV Ag/Ab combo, HIV viral load Rapid HIV test (chemistry) Lesion screen- HSV or VZV Malaria screen Measles IgG/M Norovirus NAAT Mumps IgG/M Mycology testing Rickettsial serology/Q fever Rabies Legionella culture and Urine antigen Rubella IgG/M Sacchromyces antibody Schistosoma serology (IgG) Schistosoma urine exam Stool viral food borne illness outbreak
Syphilis IgG screen Tick identification ToRC screen-serology (IgM and IgG) for Toxoplasma, Rubella and CMV Toxoplasma serology (IgG/IgM) Toxocariasis serology Varicella zoster serology (IgG/M) VDRL- CSF only Stool- H. pylori antigen Stool- parasites and ID Stool- viral cultures CSF- viral culture Tissue biopsy- viral cutlure Trichomonas NAAT Bacterial (S.pneumoniae, H. influenza, N. meningitides) PCR on CSF West nile virus serology (IgM) West nile virus CSF- PCR Yersinia serology
